PLAISTOW, N.H. — Doctors discovered that 3-year-old James Nicholson’s body was covered with bruises, including one that began on his chest and reached around to his back, and authorities now fear the child was physically abused for a longer period of time than originally thought, a prosecutor said today.

The details of the injuries suffered by the child were disclosed in Plaistow District Court today where the boy’s mother, Jessica M. Linscott, and her boyfriend, Roland H. Dow III, were each described as flight risks when they made their intial appearances via closed circuit television from the Rockingham County Jail.

Linscott, 23, and Dow, 27, were the targets of a nationwide manhunt that began Nov. 16 and ended Nov. 28 when they were captured by US marshals at the Universal Theme Park in Orlando, Fla. They were watching a parade when they were apprehended.

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The couple dropped James off at the Exeter Hospital on Nov. 14 and knew that by Nov. 16 that they were facing criminal charges, prosecutors said. Dow was charged with abusing the child and Linscott was charged with failing to stop the beatings and not getting medical help. But Rockingham Assistant County Attorney Michael Zaino said today the couple instead chose to flee the area.

He said the couple made their way first to Haverhill and then to Boston where they took a bus to New York City. From there, the couple boarded a train to Florida, he said.

Zaino also told Judge Sharon N. DeVries that doctors at two hospitals examined the child and both have independently concluded that the injuries were so severe, they could not have been self-inflicted as some of Dow’s relatives have claimed in media interviews.

He said the child was bruised on his forehead, his cheek, his right arm, buttocks, leg, lower right ankle, and he had a swelling of the brain, as the result of repeated beatings.

“One of the bruises seems to stretch from his ribcage to the middle of his back, all the way across and around his rib cage,’’ Zaino said. “Clearly he has been put in harm’s way,’’ Zaino said.

Dow is currently charged with first- and second-degree assault and five counts of endangering a child. Zaino, however, said that may change depending on the outcome of the ongoing grand jury investigation.

“There is a very strong chance that there will be more charges forthcoming when this matter is brought to the grand jury for a broader time period than is currently expressed in those charges,’’ Zaino said in court.

Linscott is facing six counts of endangering a child for allegedly allowing Dow to harm her son and for failing to get him medical help after the alleged attacks. She told the judge that she cannot afford her own lawyer and asked that one be appointed for her.

After DeVries set bail at $100,000 cash, Linscott was asked if she would be able to raise that much cash.

Linscott said she could not raise that amount of money, but also indicated she was not interested in being released because “there’s a protective order on my son, so I can’t see him anyways.’’

DeVries set bail at $500,000 cash for Dow, who has hired his own lawyer, Manchester attorney Lawrence Vogelman.

Dow, who is listed in police reports as being five foot 10 inches tall and weighing 130 pounds, had deep circles under his eyes and was ordered to live with his mother in Newton, N.H., if he posts bail.